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Bioinformatics. 2012 Aug 15;28(16):2180-1. doi: 10.1093/bioinformatics/bts337. Epub 2012 Jun 10.

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.

Author information

1
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA. sun.zhifu@mayo.edu

Abstract

Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation.

AVAILABILITY AND IMPLEMENTATION:

SAAP-RRBS is freely available to non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.

PMID:
22689387
PMCID:
PMC3413387
DOI:
10.1093/bioinformatics/bts337
[Indexed for MEDLINE]
Free PMC Article

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